## [1] "Sample size = 346"
## [1] "Loci = 244"
## [1] "1 to 130 alleles per locus per sample"
## `summarise()` has grouped output by 'sampleID', 'log_parasitemia'. You can
## override using the `.groups` argument.
## `summarise()` has grouped output by 'sampleID', 'log_parasitemia', 'plate'. You
## can override using the `.groups` argument.
## [1] "Percent dimers by sample prep date (in %, already multiplied by 100)"
## # A tibble: 4 × 2
## prep_date dimer_percent
## <chr> <dbl>
## 1 2023_03_06 0.549
## 2 2023_03_28 0.356
## 3 2023_03_30 0.458
## 4 2023_04_05 0.825
## [1] "List of pool 1A/1B/2 loci with >100 reads (summed over all negative controls)"
## # A tibble: 25 × 5
## locus reads pool Category Reason to include (if dr…¹
## <chr> <int> <chr> <chr> <chr>
## 1 Pf3D7_13_v3-2814583-2814832-2 344 2 <NA> HRP3 deletion
## 2 Pf3D7_11_v3-1902041-1902278-2 290 2 <NA> ch11
## 3 Pf3D7_13_v3-1726174-1726408-2 269 2 <NA> <NA>
## 4 Pf3D7_12_v3-2092654-2092884-2 249 2 <NA> 100
## 5 Pf3D7_13_v3-1725124-1725365-2 195 2 <NA> 613
## 6 Pf3D7_13_v3-1725887-1726123-2 176 2 <NA> <NA>
## 7 Pf3D7_13_v3-2770591-2770863-2 170 2 <NA> HRP3 deletion
## 8 Pf3D7_11_v3-1950431-1950680-2 169 2 <NA> ch11
## 9 Pf3D7_14_v3-294503-294768-2 160 2 <NA> cnv
## 10 Pf3D7_03_v3-221295-221532-2 159 2 <NA> C-terminal
## # ℹ 15 more rows
## # ℹ abbreviated name: ¹`Reason to include (if drug resistance: aminoacids)`
## [1] "Mean of total locus = 214, Mean prop. of monoclonal loci = 0.85, Mean prop. of polyclonal loci = 0.15"
## [1] "Pool 1A loci that are abset in positive controls:"
## [1] "PKNH_12_v2-198869-199113-1AB" "PmUG01_12_v1-1397996-1398245-1AB"
## [3] "PocGH01_12_v1-1106456-1106697-1AB" "PvP01_12_v1-1184983-1185208-1AB"
##
## 1A 1AB 1B 1B2 2
## 165 5 75 2 29
## [1] "No reads in any samples for these loci, for 1A"
## # A tibble: 0 × 3
## # ℹ 3 variables: locus <chr>, pool <chr>, n <dbl>
## [1] "List of samples that do not have >75% loci with >100 reads, in pool 1A"
## # A tibble: 172 × 7
## # Groups: sampleID [172]
## sampleID pool totreads n50 n100 neg_control norm
## <chr> <chr> <int> <int> <int> <lgl> <dbl>
## 1 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 235 0 0 FALSE 0
## 2 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 1989 4 0 FALSE 0
## 3 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 8057 61 18 FALSE 0.112
## 4 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 464 0 0 FALSE 0
## 5 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 989 0 0 FALSE 0
## 6 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 2786 7 0 FALSE 0
## 7 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 4984 28 6 FALSE 0.0375
## 8 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 7523 63 16 FALSE 0.1
## 9 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 9277 77 23 FALSE 0.144
## 10 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 698 0 0 FALSE 0
## # ℹ 162 more rows
##
## TRUE
## 47
## [1] "Loci without any reads, pool 5"
## # A tibble: 0 × 16
## # ℹ 16 variables: locus-pool <chr>, Category <chr>, chr_malaria <chr>,
## # ampInsert_start <dbl>, ampInsert_end <dbl>, GeneID <chr>, Gene <chr>,
## # Reason to include (if drug resistance: aminoacids) <chr>,
## # Amino acid range (*: partial coverage of that aminoacid) <chr>,
## # pool5 <lgl>, amplicon_id <chr>, amplicon_start <dbl>, amplicon_end <dbl>,
## # fwd_primer <chr>, rev_primer <chr>, n <dbl>
## [1] "List of samples that do not have >75% alleles with >100 reads, pool 5"
## # A tibble: 154 × 7
## # Groups: sampleID [154]
## sampleID pool totreads n50 n100 neg_control norm
## <chr> <chr> <int> <int> <int> <lgl> <dbl>
## 1 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 86 0 0 FALSE 0
## 2 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 647 2 0 FALSE 0
## 3 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 3216 22 10 FALSE 0.227
## 4 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 138 0 0 FALSE 0
## 5 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 364 0 0 FALSE 0
## 6 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 862 2 0 FALSE 0
## 7 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 1550 14 3 FALSE 0.0682
## 8 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 2037 18 5 FALSE 0.114
## 9 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 3295 24 15 FALSE 0.341
## 10 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 266 0 0 FALSE 0
## # ℹ 144 more rows
## Joining with `by = join_by(sampleID)`
## [1] "Sample size= 151"
## [1] "Number of entries excluded = 0, Proportion excluded = 0"
## [1] "Number of loci after cleanup = 242"
## character(0)